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| griddap | Subset | tabledap | Make A Graph | wms | files | Accessible | Title | Summary | FGDC | ISO 19115 | Info | Background Info | RSS | Institution | Dataset ID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_908689_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_908689_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_908689_v1/ | public | [Gulf of Alaska copepods: annotated transcriptomes] - Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska) | The dataset includes the annotation files of nine high-quality de novo transcriptomes generated from shotgun assemblies of short-sequence reads. The species are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. The de novo assemblies included one generated several years ago plus eight new ones generated from six co-occurring species of calanoid copepods in the Gulf of Alaska. The transcriptomes include the first published ones for Neocalanus plumchrus, Neocalanus cristatus, Eucalanus bungii and Metridia pacifica and three for Neocalanus flemingeri and two for Calanus marshallae. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Short-sequence reads were assembled with Trinity software and resulting transcripts were annotated using the SwissProt database with additional functional annotation using gene ontology terms and enzyme function. The annotations files are the first ones published for these species. The integrated dataset can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes using the annotations.\n\nThese data are further described in the following publications: Hartline, et al. (2023) (DOI: 10.1038/s41597-023-02130-1), Roncalli, et al. (2022) (DOI: 10.1111/mec.16354), and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)\n\ncdm_data_type = Other\nVARIABLES:\nseq_id (unitless)\nGenbank_accession (unitless)\nSpecies (unitless)\nStation (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\nDepth_range (meters (m))\nLife_stage (unitless)\nSex (unitless)\nEntry (unitless)\n... (20 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_908689_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_908689_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_908689_v1/index.htmlTable | https://www.bco-dmo.org/dataset/908689
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_908689_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_908689_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_908689_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_627835.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_627835 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_627835.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_627835/ | public | [Inferno vent plume proteins-Av1] - Proteins identified from the black smoker chimney Inferno hydrothermal vent plume meta-proteome - replicate Av1 - on the Axial seamount off the coast of Washington in 2011. (Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade) | Proteins identified in the Inferno hydrothermal vent plume meta-proteome\n(replicate Av1).\\u00a0 Only proteins identified by peptides with a protein\nprobability >0.9 are listed.\\u00a0\n \nThese data are reported as Supplementary Table 3 and discussed in [Mattes et\nal., 2013](\\\\http://dmoserv3.bco-\ndmo.org/data_docs/SulfurOxidizers/Mattes_2013_PlumeProt.pdf\\\\).\n(doi:10.1038/ismej.2013.113)\n \nThe FASTA information in the data was expanded to include the metadata when\nthose FASTA headers were linked to GenBank.\\u00a0\n \nProteins that were identified in biological replicate Av2 that were not\nidentified in biological replicate Av1. (GSO: Gamma Sulfur Oxidizer)\n \n \n \\u00a0\n \n\\u00a0\n \n\\u00a0\n \n\\u00a0\n \n\\u00a0\n \n\\Although fewer proteins were identified in Av2, nearly all (94%) of the\nproteins identified in Av2 were also identified in Av1.\\u00a0 Differences in\nthe total number of proteins identified in replicate samples may result from\ndifferences in the amount of biomass obtained during sample processing.\\\n \nDMO notes: \n Put multiple FASTA entries on separate lines \n Split out one number in FASTA header for linking \n Left it sorted by Total Independent Spectra column \n Added linkage column \n Removed commas in 'consensus annotation' column (signals database to put in\nnew column) \n Reordered columns to put KEGG last -- much longer than any other column\n\ncdm_data_type = Other\nVARIABLES:\nentry (number)\n... (10 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_627835_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_627835/index.htmlTable | https://www.bco-dmo.org/dataset/627835
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_627835.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_627835&showErrors=false&email= | BCO-DMO | bcodmo_dataset_627835 |